Incidental Mutation 'IGL00959:Jmjd6'
ID28598
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Jmjd6
Ensembl Gene ENSMUSG00000056962
Gene Namejumonji domain containing 6
SynonymsPtdsr, 5730436I23Rik, PtdSerR, PSR
Accession Numbers
Is this an essential gene? Essential (E-score: 1.000) question?
Stock #IGL00959
Quality Score
Status
Chromosome11
Chromosomal Location116837432-116843449 bp(-) (GRCm38)
Type of Mutationmissense
DNA Base Change (assembly) A to T at 116842376 bp
ZygosityHeterozygous
Amino Acid Change Aspartic acid to Glutamic Acid at position 115 (D115E)
Ref Sequence ENSEMBL: ENSMUSP00000115086 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000047616] [ENSMUST00000106370] [ENSMUST00000140349] [ENSMUST00000140513] [ENSMUST00000142495]
Predicted Effect probably benign
Transcript: ENSMUST00000047616
AA Change: D158E

PolyPhen 2 Score 0.416 (Sensitivity: 0.89; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000047570
Gene: ENSMUSG00000056962
AA Change: D158E

DomainStartEndE-ValueType
JmjC 141 305 6.09e-48 SMART
low complexity region 340 369 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000106370
SMART Domains Protein: ENSMUSP00000101978
Gene: ENSMUSG00000090266

DomainStartEndE-ValueType
low complexity region 5 22 N/A INTRINSIC
Pfam:Methyltransf_16 48 203 9.9e-20 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000124831
SMART Domains Protein: ENSMUSP00000122867
Gene: ENSMUSG00000056962

DomainStartEndE-ValueType
Pfam:JmjC 1 81 6.3e-20 PFAM
low complexity region 150 179 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000128784
Predicted Effect noncoding transcript
Transcript: ENSMUST00000130120
Predicted Effect probably benign
Transcript: ENSMUST00000132593
Predicted Effect probably benign
Transcript: ENSMUST00000140349
AA Change: D110E

PolyPhen 2 Score 0.051 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000120850
Gene: ENSMUSG00000056962
AA Change: D110E

DomainStartEndE-ValueType
JmjC 93 257 6.09e-48 SMART
Predicted Effect possibly damaging
Transcript: ENSMUST00000140513
AA Change: D115E

PolyPhen 2 Score 0.683 (Sensitivity: 0.86; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000115086
Gene: ENSMUSG00000056962
AA Change: D115E

DomainStartEndE-ValueType
JmjC 98 262 6.09e-48 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000140869
Predicted Effect noncoding transcript
Transcript: ENSMUST00000141735
Predicted Effect probably benign
Transcript: ENSMUST00000142495
AA Change: D158E

PolyPhen 2 Score 0.260 (Sensitivity: 0.91; Specificity: 0.88)
SMART Domains Protein: ENSMUSP00000117922
Gene: ENSMUSG00000056962
AA Change: D158E

DomainStartEndE-ValueType
JmjC 141 270 4.17e-14 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000175930
Predicted Effect noncoding transcript
Transcript: ENSMUST00000176765
Predicted Effect noncoding transcript
Transcript: ENSMUST00000176799
Predicted Effect noncoding transcript
Transcript: ENSMUST00000184052
Coding Region Coverage
Validation Efficiency
MGI Phenotype FUNCTION: This gene encodes a nuclear protein with a JmjC domain. JmjC domain-containing proteins are predicted to function as protein hydroxylases or histone demethylases. This protein functions in differentiation of multiple tissues during development, and in anti-inflammatory cytokine signaling. It was first identified as a putative phosphatidylserine receptor involved in phagocytosis of apoptotic cells; however, subsequent studies have indicated that this protein does not directly function in the clearance of apoptotic cells, and questioned whether it is a true phosphatidylserine receptor. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for disruptions in this gene show perinatal lethality. Abnormalities are observed in the nervous. respiratory, cardiovascular, digestive, renal, hematopoietic, and immune systems. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 37 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Alox12b A T 11: 69,166,243 H430L probably damaging Het
Aox4 G T 1: 58,239,174 V443F probably damaging Het
Bmpr2 A T 1: 59,815,315 I108F possibly damaging Het
Cflar G A 1: 58,729,162 probably null Het
Chchd3 A G 6: 32,968,253 V106A probably benign Het
Chl1 G T 6: 103,709,250 probably null Het
Clvs2 C T 10: 33,528,463 M252I probably benign Het
Cntnap5a T A 1: 116,184,327 L449Q probably benign Het
Col6a2 T A 10: 76,614,534 I188F probably damaging Het
Cyp2c55 A G 19: 39,038,143 D398G probably benign Het
Dennd1b T C 1: 139,143,888 probably benign Het
Dopey1 T A 9: 86,487,431 Y106N probably damaging Het
Dpy19l1 A T 9: 24,423,197 probably null Het
Extl3 C T 14: 65,076,912 V274I probably benign Het
Fras1 G A 5: 96,781,281 R3848H probably damaging Het
Gm11437 A C 11: 84,148,622 probably benign Het
Gss T A 2: 155,581,951 D2V probably damaging Het
Hnrnpm C A 17: 33,649,902 R517L probably damaging Het
Ilvbl G A 10: 78,583,905 D548N probably damaging Het
Kidins220 T A 12: 25,051,133 S1110R possibly damaging Het
Kmt2c T A 5: 25,276,229 I4784F probably damaging Het
Mrpl52 T C 14: 54,427,037 V11A possibly damaging Het
Myo3b A G 2: 70,314,292 Y1036C probably damaging Het
Olfr769 T A 10: 129,112,024 M134L probably benign Het
Omp T C 7: 98,145,150 D90G probably damaging Het
Osmr T C 15: 6,824,605 I541V probably benign Het
Ppp1r32 A T 19: 10,477,523 probably null Het
Ppp2r1a A T 17: 20,961,578 probably benign Het
Ptpn13 T A 5: 103,517,571 probably null Het
Rock2 C A 12: 16,978,055 N1429K probably benign Het
Slc25a20 T G 9: 108,681,999 M188R possibly damaging Het
Slc28a1 T C 7: 81,169,068 probably benign Het
Sult2a6 T C 7: 14,254,709 Y42C probably damaging Het
Tgfb2 A G 1: 186,704,587 V63A probably benign Het
Ugt2b38 A T 5: 87,411,823 N403K probably damaging Het
Vmn2r29 A G 7: 7,241,856 W340R probably benign Het
Wnt5a C T 14: 28,522,909 T351M probably damaging Het
Other mutations in Jmjd6
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01877:Jmjd6 APN 11 116842693 missense probably benign
IGL01941:Jmjd6 APN 11 116841358 splice site probably null
IGL02316:Jmjd6 APN 11 116843102 missense possibly damaging 0.50
IGL03396:Jmjd6 APN 11 116841251 missense probably damaging 1.00
jumanji UTSW 11 116842500 missense probably damaging 1.00
R0675:Jmjd6 UTSW 11 116840527 missense probably damaging 1.00
R1531:Jmjd6 UTSW 11 116842440 missense probably benign
R2259:Jmjd6 UTSW 11 116841314 missense probably damaging 1.00
R3937:Jmjd6 UTSW 11 116841165 missense probably benign
R4284:Jmjd6 UTSW 11 116842708 missense probably damaging 1.00
R5534:Jmjd6 UTSW 11 116840426 missense probably damaging 1.00
R5881:Jmjd6 UTSW 11 116839856 nonsense probably null
R6546:Jmjd6 UTSW 11 116842500 missense probably damaging 1.00
R7468:Jmjd6 UTSW 11 116842449 missense probably damaging 1.00
Posted On2013-04-17